This parentage verification study was carried out on 14 full-sib families of Eucalyptus species. Verification of the correct paternity and maternity is a key step in accurately estimating quantitative genetic parameters as well as efficiently genotyping for genetic linkage map construction and phenotype assessment. Six microsatellite markers were used for this certification. Out of 305 progeny individuals, 78.03% were correctly assigned to the putative mother/father trees. Variable levels of contamination were detected in 10 of the 14 families. Alternative pollen parents could be identified among the parent trees tested for 4.5% of the offspring, revealing possible mislabeling in controlled crosses. The identification of several participating pollen parents in some families suggests pollen and/or seed mixture. This study highlights that the current controlled pollination methods used in Eucalyptus are subject to errors. Parentage certification should be used on a routine basis in controlled crossing operations, especially when families are to be used for quantitative trait loci mapping.